This object implements the SearchWriterI interface which will produce a set of Text for a specific Bio::Search::Report::ReportI interface.

You can also provide the argument -filters => \%hash to filter the at the hsp, hit, or result level. %hash is an associative array which contains any or all of the keys (HSP, HIT, RESULT). The values pointed to by these keys would be references to a subroutine which expects to be passed an object - one of Bio::Search::HSP::HSPI, Bio::Search::Hit::HitI, and Bio::Search::Result::ResultI respectively. Each function needs to return a boolean value as to whether or not the passed element should be included in the output report - true if it is to be included, false if it to be omitted.

For example to filter on sequences in the database which are too short for your criteria you would do the following.

This module will use the module Text::Wrap if it is installed to wrap the Query description line. If you do not have Text::Wrap installed this module will work fine but you won't have the Query line wrapped. You will see a warning about this when you first instantiate a TextResultWriter - to avoid these warnings from showing up, simply set the verbosity upon initialization to -1 like this: my $writer = new Bio::SearchIO::Writer::TextResultWriter(-verbose => -1);

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Title : new
Usage : my $obj = Bio::SearchIO::Writer::TextResultWriter->new();
Function: Builds a new Bio::SearchIO::Writer::TextResultWriter object
Returns : Bio::SearchIO::Writer::TextResultWriter
Args : -filters => hashref with any or all of the keys (HSP HIT RESULT)
which have values pointing to a subroutine reference
which will expect to get a Hit,HSP, Result object respectively
-no_wublastlinks => boolean. Do not display WU-BLAST lines even if
they are parsed out
Links = (1)

Title : start_report
Usage : $index->start_report( CODE )
Function: Stores or returns the code to
write the start of the <HTML> block, the <TITLE> block
and the start of the <BODY> block of HTML. Useful
for (for instance) specifying alternative
HTML if you are embedding the output in
an HTML page which you have already started.
(For example a routine returning a null string).
Returns \&default_start_report (see below) if not
set.
Example : $index->start_report( \&my_start_report )
Returns : ref to CODE if called without arguments
Args : CODE

Title : title
Usage : $self->title($CODE)
Function: Stores or returns the code to provide HTML for the given
BLAST report that will appear at the top of the BLAST report
HTML output. Useful for (for instance) specifying
alternative routines to write your own titles.
Returns \&default_title (see below) if not
set.
Example : $index->title( \&my_title )
Returns : ref to CODE if called without arguments
Args : CODE

Title : default_title
Usage : $self->default_title($result)
Function: Provides HTML for the given BLAST report that will appear
at the top of the BLAST report output.
Returns : empty for text implementation
Args : First argument is a Bio::Search::Result::ResultI

Title : end_report
Usage : $self->end_report()
Function: The method to call when ending a report, this is
mostly for cleanup for formats which require you to
have something at the end of the document (</BODY></HTML>)
for HTML
Returns : string
Args : none

Title : id_parser
Usage : $index->id_parser( CODE )
Function: Stores or returns the code used by record_id to
parse the ID for record from a string. Useful
for (for instance) specifying a different
parser for different flavours of FASTA file.
Returns \&default_id_parser (see below) if not
set. If you supply your own id_parser
subroutine, then it should expect a fasta
description line. An entry will be added to
the index for each string in the list returned.
Example : $index->id_parser( \&my_id_parser )
Returns : ref to CODE if called without arguments
Args : CODE